Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/2904c590c1aef950d6935166807848/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/2904c590c1aef950d6935166807848/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/2eb6843b7950003a7c7efec56a038e/HCC1395_tumor.md.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/2eb6843b7950003a7c7efec56a038e/HCC1395_tumor.md.bam.bai
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i HCC1395_tumor.md.bam --algo AlignmentStat HCC1395_tumor.sentieon.alignment_summary_metrics --algo InsertSizeMetricAlgo HCC1395_tumor.sentieon.insert_size_metrics --algo QualDistribution HCC1395_tumor.sentieon.quality_distribution_metrics --algo BaseDistributionByCycle HCC1395_tumor.sentieon.base_distribution_by_cycle_metrics --algo MeanQualityByCycle HCC1395_tumor.sentieon.quality_by_cycle_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:164000001, elapsed 0.0s, est remaining 0.5s, peak mem 81MB, user 0.1s, sys 0.2s, output queue size 21
progress 10% @chr2:74000001, elapsed 0.0s, est remaining 0.4s, peak mem 81MB, user 0.2s, sys 0.8s, output queue size 30
progress 15% @chr2:236000001, elapsed 0.1s, est remaining 0.4s, peak mem 81MB, user 0.3s, sys 1.4s, output queue size 28
progress 20% @chr3:134000001, elapsed 0.1s, est remaining 0.3s, peak mem 81MB, user 0.3s, sys 2.0s, output queue size 19
progress 25% @chr4:116000001, elapsed 0.1s, est remaining 0.3s, peak mem 81MB, user 0.4s, sys 2.5s, output queue size 9
progress 30% @chr5:86000001, elapsed 0.1s, est remaining 0.3s, peak mem 81MB, user 0.5s, sys 3.1s, output queue size 23
progress 35% @chr6:67000001, elapsed 0.1s, est remaining 0.3s, peak mem 81MB, user 0.6s, sys 3.7s, output queue size 16
progress 40% @chr7:32000001, elapsed 0.2s, est remaining 0.3s, peak mem 81MB, user 0.7s, sys 4.2s, output queue size 23
progress 45% @chr8:59000001, elapsed 0.2s, est remaining 0.2s, peak mem 81MB, user 0.7s, sys 4.8s, output queue size 17
progress 50% @chr9:74000001, elapsed 0.2s, est remaining 0.2s, peak mem 81MB, user 0.8s, sys 5.3s, output queue size 6
progress 55% @chr10:96000001, elapsed 0.2s, est remaining 0.2s, peak mem 81MB, user 0.9s, sys 5.8s, output queue size 6
progress 60% @chr11:125000001, elapsed 0.2s, est remaining 0.2s, peak mem 81MB, user 1.0s, sys 6.4s, output queue size 10
progress 65% @chr13:16000001, elapsed 0.3s, est remaining 0.1s, peak mem 81MB, user 1.0s, sys 6.9s, output queue size 10
progress 70% @chr14:62000001, elapsed 0.3s, est remaining 0.1s, peak mem 81MB, user 1.1s, sys 7.4s, output queue size 21
progress 75% @chr16:14000001, elapsed 0.3s, est remaining 0.1s, peak mem 81MB, user 1.2s, sys 7.9s, output queue size 12
progress 80% @chr17:80000001, elapsed 0.3s, est remaining 0.1s, peak mem 81MB, user 1.3s, sys 8.4s, output queue size 22
progress 85% @chr20:23000001, elapsed 0.4s, est remaining 0.1s, peak mem 81MB, user 1.4s, sys 9.0s, output queue size 17
progress 90% @chrX:45000001, elapsed 0.4s, est remaining 0.0s, peak mem 93MB, user 1.8s, sys 9.2s, output queue size 114
progress 95% @chrY:42000001, elapsed 0.4s, est remaining 0.0s, peak mem 108MB, user 2.3s, sys 9.5s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.1s, est remaining 0.0s, peak mem 132MB, user 5.4s, sys 9.8s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: AlignmentStat InsertSizeMetricAlgo QualDistribution BaseDistributionByCycle MeanQualityByCycle
license: sentieon:Metrics=31
input file size: 50813908
reads: 1001320
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.256 user 4.941 sys 6.399 real
done: 1 calls 0.000 user 0.000 sys 0.001 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.003 user 0.003 sys 1.160 real
idle: 82 calls 0.032 user 0.037 sys 50.613 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 138567680 mem 5.603 user 10.423 sys 2.205 real